# GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

## Documentation for package ‘GENESIS’ version 2.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

GENESIS-package | GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
admixMap | admixMap
admixMapMM | Defunct functions in package 'GENESIS'
assocTestAggregate | Aggregate Association Testing
assocTestAggregate-method | Aggregate Association Testing
assocTestAggregate-methods | Aggregate Association Testing
assocTestMM | Defunct functions in package 'GENESIS'
assocTestSeq | Defunct functions in package 'GENESIS'
assocTestSeqWindow | Defunct functions in package 'GENESIS'
assocTestSingle | Genotype Association Testing with Mixed Models
assocTestSingle-method | Genotype Association Testing with Mixed Models
assocTestSingle-methods | Genotype Association Testing with Mixed Models
calcISAFBeta | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
calcScore | Fit a Model Under the Null Hypothesis
computeVSIF | Computes variant-specific inflation factors
computeVSIFNullModel | Computes variant-specific inflation factors
correctK0 | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
correctK2 | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
correctKin | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
effectAllele | Return the effect allele for association testing
effectAllele-method | Return the effect allele for association testing
effectAllele-methods | Return the effect allele for association testing
fitNullMM | Defunct functions in package 'GENESIS'
fitNullModel | Fit a Model Under the Null Hypothesis
fitNullModel-method | Fit a Model Under the Null Hypothesis
fitNullModel-methods | Fit a Model Under the Null Hypothesis
fitNullModelFastScore | Fit a Model Under the Null Hypothesis
fitNullModelFastScore-method | Fit a Model Under the Null Hypothesis
fitNullModelFastScore-methods | Fit a Model Under the Null Hypothesis
fitNullReg | Defunct functions in package 'GENESIS'
GENESIS | GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GENESIS-defunct | Defunct functions in package 'GENESIS'
HapMap_ASW_MXL_KINGmat | Matrix of Pairwise Kinship Coefficient Estimates for the combined HapMap ASW and MXL Sample found with the KING-robust estimator from the KING software.
isNullModelFastScore | Fit a Model Under the Null Hypothesis
isNullModelSmall | Fit a Model Under the Null Hypothesis
jointScoreTest | Perform a joint score test
kin2gds | Store kinship matrix in GDS
king2mat | Defunct functions in package 'GENESIS'
kingToMatrix | Convert KING text output to an R Matrix
kingToMatrix-method | Convert KING text output to an R Matrix
makeSparseMatrix | Make a sparse matrix from a dense matrix or a table of pairwise values
makeSparseMatrix-method | Make a sparse matrix from a dense matrix or a table of pairwise values
makeSparseMatrix-methods | Make a sparse matrix from a dense matrix or a table of pairwise values
mat2gds | Store kinship matrix in GDS
nullModelFastScore | Fit a Model Under the Null Hypothesis
nullModelInvNorm | Fit a Model Under the Null Hypothesis
nullModelSmall | Fit a Model Under the Null Hypothesis
pcair | PC-AiR: Principal Components Analysis in Related Samples
pcair-method | PC-AiR: Principal Components Analysis in Related Samples
pcair-methods | PC-AiR: Principal Components Analysis in Related Samples
pcairPartition | Partition a sample into an ancestry representative 'unrelated subset' and a 'related subset'
pcrelate | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
pcrelate-method | Defunct functions in package 'GENESIS'
pcrelate-method | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
pcrelateMakeGRM | Defunct functions in package 'GENESIS'
pcrelateReadInbreed | Defunct functions in package 'GENESIS'
pcrelateReadKinship | Defunct functions in package 'GENESIS'
pcrelateSampBlock | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
pcrelateToMatrix | Creates a Genetic Relationship Matrix (GRM) of Pairwise Kinship Coefficient Estimates from PC-Relate Output
pcrelateToMatrix-method | Creates a Genetic Relationship Matrix (GRM) of Pairwise Kinship Coefficient Estimates from PC-Relate Output
plot.pcair | PC-AiR: Plotting PCs
print.pcair | PC-AiR: Principal Components Analysis in Related Samples
print.summary.pcair | PC-AiR: Principal Components Analysis in Related Samples
samplesGdsOrder | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
sample_annotation_1KG | Annotation for 1000 genomes Phase 3 samples
summary.pcair | PC-AiR: Principal Components Analysis in Related Samples
varCompCI | Variance Component Confidence Intervals